<html>
<head>
<meta NAME="description" CONTENT="IUPAC InChI format in Marvin">
<meta NAME="keywords" CONTENT="IUPAC, InChI, Java, Marvin">
<meta NAME="author" CONTENT="Peter Vadasz">
<link REL ="stylesheet" TYPE="text/css" HREF="../marvinmanuals.css" TITLE="Style">
<title> IUPAC InChI in Marvin </title>
</head>

<body>
<h1>IUPAC InChI and InChIKey</h1>

<p>
Codename: <strong>inchi, inchikey</strong>
</p>
<h2>Contents</h2>
<ul>
<li><a href="#inchi">IUPAC InChi format</a></li>
<li><a href="#options">Export options</a></li>
<li><a href="#references">References</a></li>
</ul>

<h2><a class="anchor" name="inchi">IUPAC InChI format</a></h2>
<p>
The Marvin beans and applications are able to import and export IUPAC InChI
files, and export IUPAC InChIKey files. This function does not work in the
applets (except signed applets).
</p>
<p>
The export makes an inchi with AuxInfo by default. The import requires an 
inchi string (AuxInfo is optional). Without AuxInfo, the generated molecule
does not include coordinates.
</p>
<p>
At the moment Linux, Windows and Mac platforms are supported, but we will
also add Sun and possibly HP Unix.
</p>
<p>
Since Marvin 5.2.2 the InChI 1.02 version is integrated, which enables to 
export InChiKey as an export option, since Marvin 5.2.5 InChIKey export format
is also added.
</p>

<h2><a class="anchor" NAME="options">Export options</a></h2>
<p>
Export options can be specified in the format string. The format descriptor
and the options are separated by a colon, the options by commas.
</p>

<blockquote>
<table CELLSPACING=10 CELLPADDING=0>
<tr VALIGN="TOP">
    <td NOWRAP>...</td>
    <td><a class="text" HREF="basic-export-opts.html">Basic options for aromatization and
	H atom adding/removal</a></td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_SNon"><strong>SNon</strong></a></td>
    <td>Exclude stereo (Deafult: Include Absolute stereo)</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_SRel"><strong>SRel</strong></a></td>
    <td>Relative stereo</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_SRac"><strong>SRac</strong></a></td>
    <td>Racemic stereo</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_SUCF"><strong>SUCF</strong></a></td>
    <td>Use Chiral Flag: On means Absolute stereo, Off - Relative</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_SUU"><strong>SUU</strong></a></td>
    <td>Include omitted unknown/undefined stereo</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_NEWPS"><strong>NEWPS</strong></a></td>
    <td>Narrow end of wedge points to stereocenter (default: both)</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_RecMet"><strong>RecMet</strong></a></td>
    <td>Include reconnected metals results</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_FixedH"><strong>FixedH</strong></a></td>
    <td>Mobile H Perception Off (Default: On)</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_AuxNone"><strong>AuxNone</strong></a></td>
    <td>Omit auxiliary information (default: Include)</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_NoADP"><strong>NoADP</strong></a></td>
    <td>Disable Aggressive Deprotonation (for testing only)</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_Compress"><strong>Compress</strong></a></td>
    <td>Compressed output</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_DoNotAddH"><strong>DoNotAddH</strong></a></td>
    <td>Don't add H according to usual valences: all H are explicit</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_Tabbed"><strong>Tabbed</strong></a></td>
    <td>Separate structure number, InChI, and AuxIndo with tabs</td></tr>
<tr VALIGN="TOP">
    <td><a class="text" NAME="option_Key"><strong>Key</strong></a></td>
    <td>Exports the InChIKey as well</td></tr>
</table>
</blockquote>

<h2><a class="anchor" NAME="knownissues">Known Issues</a></h2>
<p>
<ul>
<li>On some 64-bit machines the InChI import/export module does not 
work, since the native code is not able to run.</li>
</ul>
</p>

<h2><a class="anchor" name="references">References</a></h2>

<ul>
<li><a HREF="http://www.iupac.org/">www.iupac.org</a></li>
<li><a HREF="http://www.iupac.org/inchi/">www.iupac.org/inchi</a></li>
<li><a HREF="http://sourceforge.net/projects/inchi">sourceforge.net/projects/inchi</a></li>
</ul>

<p ALIGN=LEFT>
<small>InchiExport uses the <em>InChI format</em>,
<a HREF="../license/IUPACInChI.license.txt">InChITM Material is &copy; IUPAC 2005</a>
</small>
</p>


</body>
</html>
